.TH g_chi 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_chi - calculates everything you want to know about chi and other dihedrals

.B VERSION 4.5
.SH SYNOPSIS
\f3g_chi\fP
.BI "\-s" " conf.gro "
.BI "\-f" " traj.xtc "
.BI "\-o" " order.xvg "
.BI "\-p" " order.pdb "
.BI "\-ss" " ssdump.dat "
.BI "\-jc" " Jcoupling.xvg "
.BI "\-corr" " dihcorr.xvg "
.BI "\-g" " chi.log "
.BI "\-ot" " dihtrans.xvg "
.BI "\-oh" " trhisto.xvg "
.BI "\-rt" " restrans.xvg "
.BI "\-cp" " chiprodhisto.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-r0" " int "
.BI "\-[no]phi" ""
.BI "\-[no]psi" ""
.BI "\-[no]omega" ""
.BI "\-[no]rama" ""
.BI "\-[no]viol" ""
.BI "\-[no]periodic" ""
.BI "\-[no]all" ""
.BI "\-[no]rad" ""
.BI "\-[no]shift" ""
.BI "\-binwidth" " int "
.BI "\-core_rotamer" " real "
.BI "\-maxchi" " enum "
.BI "\-[no]normhisto" ""
.BI "\-[no]ramomega" ""
.BI "\-bfact" " real "
.BI "\-[no]chi_prod" ""
.BI "\-[no]HChi" ""
.BI "\-bmax" " real "
.BI "\-acflen" " int "
.BI "\-[no]normalize" ""
.BI "\-P" " enum "
.BI "\-fitfn" " enum "
.BI "\-ncskip" " int "
.BI "\-beginfit" " real "
.BI "\-endfit" " real "
.SH DESCRIPTION
\&g_chi computes phi, psi, omega and chi dihedrals for all your 
\&amino acid backbone and sidechains.
\&It can compute dihedral angle as a function of time, and as
\&histogram distributions.
\&The distributions (histo\-(dihedral)(RESIDUE).xvg) are cumulative over all residues of each type.


\&If option \fB \-corr\fR is given, the program will
\&calculate dihedral autocorrelation functions. The function used
\&is C(t) =  cos(chi(tau)) cos(chi(tau+t)) . The use of cosines
\&rather than angles themselves, resolves the problem of periodicity.
\&(Van der Spoel & Berendsen (1997), \fB Biophys. J. 72\fR, 2032\-2041).
\&Separate files for each dihedral of each residue
\&(corr(dihedral)(RESIDUE)(nresnr).xvg) are output, as well as a
\&file containing the information for all residues (argument of \fB \-corr\fR).


\&With option \fB \-all\fR, the angles themselves as a function of time for
\&each residue are printed to separate files (dihedral)(RESIDUE)(nresnr).xvg.
\&These can be in radians or degrees.


\&A log file (argument \fB \-g\fR) is also written. This contains 

\&(a) information about the number of residues of each type.

\&(b) The NMR 3J coupling constants from the Karplus equation.

\&(c) a table for each residue of the number of transitions between 
\&rotamers per nanosecond,  and the order parameter S2 of each dihedral.

\&(d) a table for each residue of the rotamer occupancy.

\&All rotamers are taken as 3\-fold, except for omegas and chi\-dihedrals
\&to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu
\&and gln, and chi4 of arg), which are 2\-fold. "rotamer 0" means 
\&that the dihedral was not in the core region of each rotamer. 
\&The width of the core region can be set with \fB \-core_rotamer\fR


\&The S2 order parameters are also output to an xvg file
\&(argument \fB \-o\fR ) and optionally as a pdb file with
\&the S2 values as B\-factor (argument \fB \-p\fR). 
\&The total number of rotamer transitions per timestep
\&(argument \fB \-ot\fR), the number of transitions per rotamer
\&(argument \fB \-rt\fR), and the 3J couplings (argument \fB \-jc\fR), 
\&can also be written to .xvg files.


\&If \fB \-chi_prod\fR is set (and maxchi  0), cumulative rotamers, e.g.
\&1+9(chi1\-1)+3(chi2\-1)+(chi3\-1) (if the residue has three 3\-fold 
\&dihedrals and maxchi = 3)
\&are calculated. As before, if any dihedral is not in the core region,
\&the rotamer is taken to be 0. The occupancies of these cumulative 
\&rotamers (starting with rotamer 0) are written to the file
\&that is the argument of \fB \-cp\fR, and if the \fB \-all\fR flag
\&is given, the rotamers as functions of time
\&are written to chiproduct(RESIDUE)(nresnr).xvg 
\&and their occupancies to histo\-chiproduct(RESIDUE)(nresnr).xvg.


\&The option \fB \-r\fR generates a contour plot of the average omega angle
\&as a function of the phi and psi angles, that is, in a Ramachandran plot
\&the average omega angle is plotted using color coding.
.SH FILES
.BI "\-s" " conf.gro" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-o" " order.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-p" " order.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-ss" " ssdump.dat" 
.B Input, Opt.
 Generic data file 

.BI "\-jc" " Jcoupling.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-corr" " dihcorr.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-g" " chi.log" 
.B Output
 Log file 

.BI "\-ot" " dihtrans.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oh" " trhisto.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-rt" " restrans.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-cp" " chiprodhisto.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-r0"  " int" " 1" 
 starting residue

.BI "\-[no]phi"  "no    "
 Output for Phi dihedral angles

.BI "\-[no]psi"  "no    "
 Output for Psi dihedral angles

.BI "\-[no]omega"  "no    "
 Output for Omega dihedrals (peptide bonds)

.BI "\-[no]rama"  "no    "
 Generate Phi/Psi and Chi1/Chi2 ramachandran plots

.BI "\-[no]viol"  "no    "
 Write a file that gives 0 or 1 for violated Ramachandran angles

.BI "\-[no]periodic"  "yes   "
 Print dihedral angles modulo 360 degrees

.BI "\-[no]all"  "no    "
 Output separate files for every dihedral.

.BI "\-[no]rad"  "no    "
 in angle vs time files, use radians rather than degrees.

.BI "\-[no]shift"  "no    "
 Compute chemical shifts from Phi/Psi angles

.BI "\-binwidth"  " int" " 1" 
 bin width for histograms (degrees)

.BI "\-core_rotamer"  " real" " 0.5   " 
 only the central \-core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)

.BI "\-maxchi"  " enum" " 0" 
 calculate first ndih Chi dihedrals: \fB 0\fR, \fB 1\fR, \fB 2\fR, \fB 3\fR, \fB 4\fR, \fB 5\fR or \fB 6\fR

.BI "\-[no]normhisto"  "yes   "
 Normalize histograms

.BI "\-[no]ramomega"  "no    "
 compute average omega as a function of phi/psi and plot it in an xpm plot

.BI "\-bfact"  " real" " \-1    " 
 B\-factor value for pdb file for atoms with no calculated dihedral order parameter

.BI "\-[no]chi_prod"  "no    "
 compute a single cumulative rotamer for each residue

.BI "\-[no]HChi"  "no    "
 Include dihedrals to sidechain hydrogens

.BI "\-bmax"  " real" " 0     " 
 Maximum B\-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X\-Ray structures is analyzed. \-bmax = 0 means no limit.

.BI "\-acflen"  " int" " \-1" 
 Length of the ACF, default is half the number of frames

.BI "\-[no]normalize"  "yes   "
 Normalize ACF

.BI "\-P"  " enum" " 0" 
 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR

.BI "\-fitfn"  " enum" " none" 
 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR

.BI "\-ncskip"  " int" " 0" 
 Skip N points in the output file of correlation functions

.BI "\-beginfit"  " real" " 0     " 
 Time where to begin the exponential fit of the correlation function

.BI "\-endfit"  " real" " \-1    " 
 Time where to end the exponential fit of the correlation function, \-1 is until the end

.SH KNOWN PROBLEMS
\- Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.

\- Phi and psi dihedrals are calculated in a non\-standard way, using H\-N\-CA\-C for phi instead of C(\-)\-N\-CA\-C, and N\-CA\-C\-O for psi instead of N\-CA\-C\-N(+). This causes (usually small) discrepancies with the output of other tools like g_rama.

\- \-r0 option does not work properly

\- Rotamers with multiplicity 2 are printed in chi.log as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
